Merge branch 'main' into release

griffithlab · Jul 25, 2024 · 16f3ecc · 16f3ecc
2 parents 31e8e08 + 8509b02
commit 16f3ecc
Show file tree

Hide file tree

Showing 51 changed files with 2,503 additions and 836 deletions.
diff --git a/.codespellignore b/.codespellignore
@@ -1,2 +1,3 @@
 iif
 mane
+checkin
diff --git a/client/src/app/components/diseases/my-disease-info/my-disease-info.component.html b/client/src/app/components/diseases/my-disease-info/my-disease-info.component.html
@@ -76,13 +76,18 @@
       <ng-container *ngSwitchCase="1">
         <div class="tab-padding">
           <nz-row [nzGutter]="8">
-            <nz-col [nzSpan]="12">
-              <nz-descriptions nzSize="small" [nzBordered]="true" [nzColumn]="2">
+            <nz-col [nzSpan]="24">
+              <nz-descriptions nzSize="small" [nzBordered]="true" [nzColumn]="1">
                 <nz-descriptions-item nzTitle="Definition">
                   <ng-container *ngIf="diseaseInfo.mondoDef; else noValue">
                     {{diseaseInfo.mondoDef}}
                   </ng-container>
                 </nz-descriptions-item>
+                <nz-descriptions-item nzTitle="ID">
+                  <ng-container *ngIf="diseaseInfo.mondoId; else noValue">
+                    {{diseaseInfo.mondoId}}
+                  </ng-container>
+                </nz-descriptions-item>
               </nz-descriptions>
             </nz-col>
           </nz-row>

diff --git a/client/src/app/components/layout/quicksearch/quicksearch-component.html b/client/src/app/components/layout/quicksearch/quicksearch-component.html
@@ -8,14 +8,15 @@
   nzPlaceHolder="Search CIViC"
   [nzOptionHeightPx]="28"
   [nzShowArrow]="false"
+  [nzDropdownRender]="searchEntities"
   [nzDropdownMatchSelectWidth]="false">
   <nz-option
     *ngFor="let o of (option$ | ngrxPush)"
     nzCustomContent
     [nzValue]="o.result">
     <i
       nz-icon
-      style="margin-right: 0.5em;"
+      style="margin-right: 0.5em"
       nzTheme="twotone"
       [nzTwotoneColor]="converter(o.result.resultType) | entityColor"
       [nzType]="o.result.resultType | iconNameForSubscribableEntity"></i>
@@ -39,3 +40,26 @@
     Loading Data...
   </nz-option>
 </nz-select>
+
+<ng-template #searchEntities>
+  <hr />
+  <nz-checkbox-wrapper (nzOnChange)="selectedEntitiesChanged($event)">
+    <div class="entity-select">
+      @for(entity of searchableEntities; track entity) {
+      <label
+        nz-checkbox
+        [nzValue]="entity"
+        nz-tooltip
+        [nzTooltipTitle]="entity"
+        [ngModel]="isSelected(entity)">
+        <i
+          nz-icon
+          nzTheme="twotone"
+          nzTool
+          [nzTwotoneColor]="entity | entityColor"
+          [nzType]="entity | iconNameForSubscribableEntity"></i>
+      </label>
+      }
+    </div>
+  </nz-checkbox-wrapper>
+</ng-template>
diff --git a/client/src/app/components/layout/quicksearch/quicksearch-component.less b/client/src/app/components/layout/quicksearch/quicksearch-component.less
@@ -5,3 +5,13 @@
 nz-select {
   width: 100%;
 }
+
+hr {
+  border-color: #6666
+}
+
+.entity-select {
+  margin-right: 10px;
+  margin-left: 10px;
+
+}
diff --git a/client/src/app/components/layout/quicksearch/quicksearch-component.ts b/client/src/app/components/layout/quicksearch/quicksearch-component.ts
@@ -49,6 +49,10 @@ export class CvcQuicksearchComponent {
   @ViewChild(NzSelectComponent, { static: true })
   selectNode!: NzSelectComponent
 
+  selectedEntities: SearchableEntities[] = Object.values(SearchableEntities)
+  searchableEntities = Object.keys(SearchableEntities)
+  currentSearchTerm?: string
+
   // SOURCE STREAMS
   onSearch$: Subject<string>
   onSelect$: Subject<void>
@@ -62,25 +66,29 @@ export class CvcQuicksearchComponent {
   option$: Observable<QuicksearchOption[]>
   isLoading$: Observable<boolean>
 
-
   converter = entityTypeToTypename
 
-  constructor(private gql: QuicksearchGQL, private router: Router) {
+  constructor(
+    private gql: QuicksearchGQL,
+    private router: Router
+  ) {
     this.onSearch$ = new Subject<string>()
     this.onSelect$ = new Subject<void>()
 
     this.response$ = this.onSearch$.pipe(
       skip(1), // drop initial empty string from input init
       throttleTime(300, asyncScheduler, { leading: false, trailing: true }),
       switchMap((str: string) => {
+        this.currentSearchTerm = str
+        let selectedEntities = this.selectedEntities
         // if queryRef doesn't exist, create it with watchQuery observable
         // if it does, refetch with fetchQuery observable.
         // using defer() ensures functions are not called until
         // values are emitted. otherwise they'll be called on subscribe.
         return iif(
           () => this.queryRef === undefined, // predicate
-          defer(() => watchQuery(str)), // true
-          defer(() => fetchQuery(str))
+          defer(() => watchQuery(str, selectedEntities)), // true
+          defer(() => fetchQuery(str, selectedEntities))
         ) // false
       })
     )
@@ -114,14 +122,19 @@ export class CvcQuicksearchComponent {
     })
 
     // set queryRef with watch(), return its valueChanges observable
-    const watchQuery = (str: string) => {
-      this.queryRef = this.gql.watch({ query: str, highlightMatches: true })
+    const watchQuery = (str: string, entities: Maybe<SearchableEntities[]>) => {
+      this.queryRef = this.gql.watch({
+        query: str,
+        highlightMatches: true,
+        types: entities,
+      })
       return this.queryRef.valueChanges
     }
 
     // return observable from refetch() promise
-    const fetchQuery = (str: string) =>
-      from(this.queryRef.refetch({ query: str }))
+    const fetchQuery = (str: string, entities: Maybe<SearchableEntities[]>) => {
+      return from(this.queryRef.refetch({ query: str, types: entities }))
+    }
   }
 
   urlForResult(res: SearchResult): string {
@@ -136,10 +149,28 @@ export class CvcQuicksearchComponent {
       case SearchableEntities.MolecularProfile:
         name = 'molecular-profiles'
         break
+      case SearchableEntities.Therapy:
+        name = 'therapies'
+        break
       default:
         name = `${res.resultType.toLowerCase()}s`
     }
 
     return `/${name}/${res.id}/summary`
   }
+
+  selectedEntitiesChanged(selectedEntities: string[]) {
+    this.selectedEntities = selectedEntities.map(
+      (x) => SearchableEntities[x as keyof typeof SearchableEntities]
+    )
+
+    if (this.currentSearchTerm) {
+      this.onSearch$.next(this.currentSearchTerm)
+    }
+  }
+
+  isSelected(entity: string): boolean {
+    const x = SearchableEntities[entity as keyof typeof SearchableEntities]
+    return this.selectedEntities.includes(x)
+  }
 }
diff --git a/client/src/app/components/layout/quicksearch/quicksearch.module.ts b/client/src/app/components/layout/quicksearch/quicksearch.module.ts
@@ -11,6 +11,8 @@ import { FormsModule } from '@angular/forms'
 import { NzSelectModule } from 'ng-zorro-antd/select'
 import { NzTypographyModule } from 'ng-zorro-antd/typography'
 import { CvcPipesModule } from '@app/core/pipes/pipes.module'
+import { NzCheckboxModule } from 'ng-zorro-antd/checkbox'
+import { NzToolTipModule } from 'ng-zorro-antd/tooltip'
 
 @NgModule({
   declarations: [CvcQuicksearchComponent],
@@ -27,6 +29,8 @@ import { CvcPipesModule } from '@app/core/pipes/pipes.module'
     NzFormModule,
     NzIconModule,
     NzAutocompleteModule,
+    NzCheckboxModule,
+    NzToolTipModule,
   ],
   exports: [CvcQuicksearchComponent],
 })

diff --git a/...t/src/app/components/organizations/organizations-table/organizations-table.component.html b/...t/src/app/components/organizations/organizations-table/organizations-table.component.html
@@ -51,17 +51,26 @@
           [nzSortFn]="true">
           Organization
         </th>
-        <th nzWidth="100px">Members</th>
+        <th
+          nzWidth="100px"
+          [nzColumnKey]="sortColumns.MemberCount"
+          [nzSortFn]="true">
+          Members
+        </th>
         <th nzWidth="320px">Sub Organizations</th>
         <th
           nzWidth="80px"
           nzRight
+          [nzColumnKey]="sortColumns.ActivityCount"
+          [nzSortFn]="true"
           nzAlign="right">
           Actions
         </th>
         <th
           nzWidth="125px"
           nzRight
+          [nzColumnKey]="sortColumns.MostRecentActivityTimestamp"
+          [nzSortFn]="true"
           nzAlign="right">
           Last Action
         </th>
@@ -97,13 +106,13 @@
             <cvc-tag-overflow
               [maxDisplayCount]="1"
               tagType="organization"
-              [tags]="organization.subGroups">
+              [tags]="organization.childOrganizations">
             </cvc-tag-overflow>
           </td>
           <td
             nzRight
             nzAlign="right">
-            {{ organization.eventCount | number }}
+            {{ organization.activityCount | number }}
           </td>
           <td
             nzRight

diff --git a/client/src/app/components/organizations/organizations-table/organizations-table.component.ts b/client/src/app/components/organizations/organizations-table/organizations-table.component.ts
@@ -14,7 +14,7 @@ import { ScrollEvent } from '@app/directives/table-scroll/table-scroll.directive
 import {
   Maybe,
   OrganizationBrowseTableRowFieldsFragment,
-  OrganizationConnection,
+  BrowseOrganizationConnection,
   OrganizationsBrowseGQL,
   OrganizationsBrowseQuery,
   OrganizationsBrowseQueryVariables,
@@ -70,7 +70,7 @@ export class CvcOrganizationsTableComponent implements OnInit {
     OrganizationsBrowseQueryVariables
   >
   result$!: Observable<ApolloQueryResult<OrganizationsBrowseQuery>>
-  connection$!: Observable<OrganizationConnection>
+  connection$!: Observable<BrowseOrganizationConnection>
 
   // PRESENTATION STREAMS
   pageInfo$!: Observable<PageInfo>
@@ -126,7 +126,7 @@ export class CvcOrganizationsTableComponent implements OnInit {
     this.connection$ = this.result$.pipe(
       pluck('data', 'organizations'),
       filter(isNonNulled)
-    ) as Observable<OrganizationConnection>
+    ) as Observable<BrowseOrganizationConnection>
 
     // entity row nodes
     this.row$ = this.connection$.pipe(

diff --git a/client/src/app/components/organizations/organizations-table/organizations-table.query.gql b/client/src/app/components/organizations/organizations-table/organizations-table.query.gql
@@ -32,19 +32,19 @@ query OrganizationsBrowse(
   }
 }
 
-fragment OrganizationBrowseTableRowFields on Organization {
+fragment OrganizationBrowseTableRowFields on BrowseOrganization {
   id
   name
   description
-  # profileImagePath(size: 256) @include(if: $cardView)
   url
   memberCount
-  eventCount
-  subGroups {
-    name
+  activityCount
+  mostRecentActivityTimestamp
+  childOrganizations {
     id
+    name
   }
-  mostRecentActivityTimestamp
+  # profileImagePath(size: 256) @include(if: $cardView)
   # orgStatsHash @include(if: $cardView) {
   #   comments
   #   revisions

diff --git a/client/src/app/components/users/users-table/users-table.component.html b/client/src/app/components/users/users-table/users-table.component.html
@@ -75,6 +75,8 @@
           nzRight
           nzAlign="right"
           nz-tooltip
+          [nzColumnKey]="sortColumns.EvidenceCount"
+          [nzSortFn]="true"
           nzTooltipTitle="Evidence Count">
           <i
             nz-icon
@@ -86,6 +88,8 @@
           nzRight
           nzAlign="right"
           nz-tooltip
+          [nzColumnKey]="sortColumns.RevisionCount"
+          [nzSortFn]="true"
           nzTooltipTitle="Revision Count">
           <i
             nz-icon
@@ -184,12 +188,12 @@
           <td
             nzRight
             nzAlign="right">
-            {{ user.statsHash.submittedEvidenceItems }}
+            {{ user.evidenceCount }}
           </td>
           <td
             nzRight
             nzAlign="right">
-            {{ user.statsHash.revisions }}
+            {{ user.revisionCount }}
           </td>
         </tr>
       </ng-template>

diff --git a/client/src/app/components/users/users-table/users-table.component.ts b/client/src/app/components/users/users-table/users-table.component.ts
@@ -17,7 +17,7 @@ import {
   PageInfo,
   SortDirection,
   UserBrowseTableRowFieldsFragment,
-  UserConnection,
+  BrowseUserConnection,
   UserRole,
   UsersBrowseGQL,
   UsersBrowseQuery,
@@ -71,7 +71,7 @@ export class CvcUsersTableComponent implements OnInit {
   // INTERMEDIATE STREAMS
   queryRef!: QueryRef<UsersBrowseQuery, UsersBrowseQueryVariables>
   result$!: Observable<ApolloQueryResult<UsersBrowseQuery>>
-  connection$!: Observable<UserConnection>
+  connection$!: Observable<BrowseUserConnection>
 
   // PRESENTATION STREAMS
   pageInfo$!: Observable<PageInfo>
@@ -130,7 +130,7 @@ export class CvcUsersTableComponent implements OnInit {
     this.connection$ = this.result$.pipe(
       pluck('data', 'users'),
       filter(isNonNulled)
-    ) as Observable<UserConnection>
+    ) as Observable<BrowseUserConnection>
 
     // entity row nodes
     this.row$ = this.connection$.pipe(

diff --git a/client/src/app/components/users/users-table/users-table.query.gql b/client/src/app/components/users/users-table/users-table.query.gql
@@ -34,19 +34,18 @@ query UsersBrowse(
   }
 }
 
-fragment UserBrowseTableRowFields on User {
+fragment UserBrowseTableRowFields on BrowseUser {
   id
   name
   displayName
+  username
   organizations {
     id
     name
   }
   role
-  statsHash {
-    submittedEvidenceItems
-    revisions
-  }
+  evidenceCount
+  revisionCount
   profileImagePath(size: 64)
   mostRecentActivityTimestamp
 }
diff --git a/client/src/app/core/pipes/icon-name-for-subscribable-entity.ts b/client/src/app/core/pipes/icon-name-for-subscribable-entity.ts
@@ -31,11 +31,17 @@ export class IconNameForSubscribableEntity implements PipeTransform {
       case SubscribableEntities.VariantGroup:
       case 'VARIANT_GROUP':
       case 'VariantGroup':
-        return 'civic-variant-group'
+        return 'civic-variantgroup'
       case SubscribableEntities.MolecularProfile:
       case 'MOLECULAR_PROFILE':
       case 'MolecularProfile':
         return 'civic-molecularprofile'
+      case 'THERAPY':
+      case 'Therapy':
+        return 'civic-therapy'
+      case 'DISEASE':
+      case 'Disease':
+        return 'civic-disease'
       default:
         console.log('String No icon name found for ' + e)
         return 'border-outer'